Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataattttaatactaataaatacttgtcttgtggtttatctagatggcctaacttttggaaatgtactcttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g47860.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G147430_T02 (Zea mays), 5'ss of exon 5
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataattttaatactaataaatacttgtcttgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 ||||||||||| || ||||| ||| |||| |||||||| || || |||||||||||||||||||| |||||||||||||||||||||||||||||||||||| || |||   |   |  |||       |     ||     |  | || |       || | || |  || |  | |||  |||||  | |||  || |         | |||||  |   ||  ||  || ||||  |  ||| |||||||
CAAGGCTTTCATCGAACCAGATTTGGAGACCGCACATATTAAGATCATCAACAAGTTCAACCCATTTTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaggc-ctctcaagaaaaattc------ataattctgcaccagtgacatagt------ttcaactttcaacaaccaacatt-ttttatgattaaccaagaaa------attgtttaatt--gtgcactgcctgttggtcacatacacttgcag

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143804_T01 (Zea mays), 5'ss of exon 2
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgtt-ttggcaagatggctgatcattgatctcttcaccaatagcataattttaatactaataa-atacttgtcttgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||||||||||| |||||| |||||||||||||||||||||||||| ||| |||   |      ||  |    |      | |||   ||| ||| |      ||  ||  |   || ||||| |  ||  ||  | |    | || ||| | ||| | |    | |  ||                                
CAAGGCTTTCATCGAACCAGATTTACAGACCGCACATATTAAAATCATTAACAAGTTCAACCCATGCTCAGGTTTCCAAAATCCTATGTACATTCTAAAAgtaggcatctcaagaaaattgtagaatgtacaccaatgacattgtcaacaacaaacattttttgtga-ttaaccaagaaaattgttgaattgtgcacaacatattggtcatatacact-tgcag--------------------------------

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G09660.1 (Glycine max), 5'ss of exon 5
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataattttaatactaataaatacttgtcttgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 ||||| || || ||||||||  | |||||||||||||||||||| |||||||| ||||| |||||  | || ||||| | |||||  || ||  ||||||| ||  ||   || | |       |||    ||||    |||   | |||   |   |   |          || || ||| || |  |  |  | |    |||   | ||     |||  |||    | | |||| | |  |  ||| |   
CAAGGCATTTATCGAGCCAGATCTCCAGACAGCACATATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTACTTATATATTAAAGgttagttctatataataactcattattttaaatccac---ttgtataaatgaaaggagaaaaa----------aaaaggatagttctgttggttctgatg--ttgatgtctgac--gtcttaatgaaaaatcctttgtataactgttctag---

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G14110.1 (Glycine max), 5'ss of exon 5
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataatttta-atactaataaatacttgtct-tgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 ||||| || || ||||||||  | ||||||||||| |||||||| |||||||| ||||| |||||  | || ||||| | |||||  |||||  |||||||||  |||| ||||||    |||  |   |||  |  |    | | ||     |   | |  | |     |  ||       | | | ||  |||| || | |  | | | |   |  |||||                                
CAAGGCATTTATCGAGCCAGATCTCCAGACAGCACACATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTACTTACATATTAAAGgtaataactcattattttaaatccact---tgtataaatgaaaggaggaaaaacggatagttctgttggttctgatgttgatgtgtgacatcttaatgaaaaatcctttgtataactgttctag--------------------------------

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 5'ss of exon 4
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttcctttta-gtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataattttaatactaataaatacttgtcttgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 |||||||| |||||||||||  | || ||||||||||||||||| |||||||| ||||| |||||| | || || || || || |  || ||| | |||||   |    ||  |||| ||    |||   ||    ||| || |     |  |       | |    ||  | | ||   ||                                                                        
CAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCACTTATATTTTGAAGgttgac----ctcctttaagtcgaatttgtatgcttgtgtattcgttgtcttccatggttctaagtgtttttctattattgtag-----------------------------------------------------------------------

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 5'ss of exon 4
TAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactccttatttatgttccttttagtgtccatgttttggcaagatggctgatcattgatctcttcaccaatagcataattt-taatactaataaatacttgtc-ttgtggtttatctagatggcctaacttttggaaatgtactcttgcag
 |||||||| |||||||||||  |    ||||||||||||||||| | ||| ||||||||||||||| | || || || | ||| |  || ||| | ||||| ||  | |   | |||| ||| |  | ||  ||||  |    | | | |  |   | ||| |||    | | ||| | |  |   |   ||| |    ||  | |  |||| |                                         
CAAGGCTTTTATTGAGCCAGATCTCGGAACAGCACATATAAAAATCACCAATAAGTTCAACCCATTCACTGGATTTCAGAGTCCCACTTATATTTTGAAGgtcagtgccc---aattattttcttactggtcaccataat--aaccaaaagttt---ctttggtctgg--agctatatctttgtccatgtcactgagtggtaactataattgtag-----------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|218492625|gb|FG962240.1|FG962240
EST:     ACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAG                         TCTCCACGAACTATAACACCTACTGACATCAAAGTTGCTCTTGGTGAAGAT
genomic: ACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactc ... actcttgcagTCTCCACGAACTATAACACCTACTGACATCAAAGTTGCTCTTGGTGAAGAT
EST: gi|428928|gb|D25084.1|D25084
EST:     ACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAG                         TCTCCACGAACTATAACACCTACTGACATCAAAGTTGCTCTTGGTGAAGAT
genomic: ACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTATGTACATTCTAAAGgtaagcactc ... actcttgcagTCTCCACGAACTATAACACCTACTGACATCAAAGTTGCTCTTGGTGAAGAT